Barahona was strangled with an electrical cord and little Miguel, 4, was drowned in the bathtub.

Infante, 23, initially played dumb with cops, pretending to be a grieving father, sources said. But his story quickly fell apart, and cops saw him on surveillance video entering the West 153rd Street apartment and leaving in a different set of clothes, sources said.

Cops in Bethlehem, Pa., where he now lives, executed a search warrant on Infante’s home.

He was charged with both murders Tuesday night and was awaiting arraignment at Manhattan Criminal Court.

Felicia BarahonaFacebook

His arrest is a stunning turn in a sex scandal that made headlines in 2013, when school officials revealed that Barahona repeatedly slept with Infante and had his baby.

She told the teen “not to worry” about using protection during their five-times-a-week trysts, according to a report by the city’s Special Commissioner of Investigation.

Barahona, then 32, at first flirted with Infante on Facebook and then in October 2011 invited him to a McDonald’s near Columbus Circle with her young daughter in tow.

They all went to a Disney store together, according to the report.

Miguel BarahonaFacebook

Shortly after their first “date,’’ the teacher told Infante that she wanted to kiss him — but restrained herself because the child was there, papers state.

They left each other that day without any intimate contact.

Once Infante turned 17, they were having sex on a regular basis.

Barahona found out she was pregnant in 2011, when Infante accompanied her to a doctor.

The boy told investigators that “he embraced the idea of being a father.”

With the child due in August 2012, Infante moved in with Barahona that January to prepare for the birth, papers state.

But a few weeks later there was trouble, when Infante objected to Barahona’s plans to take the child out of the country to visit her family after the birth.

Infante told investigators the end came when Barahona’s mother found him drinking rum in their home and told her daughter.

They broke up before Miguel was born.

Barahona claimed to investigators they had lived together for only a few days and split up because he didn’t get along with her daughter.

She said by then the pair had fallen in love and purchased wedding rings in anticipation of a future marriage.

Soon after the split, a despondent Infante told an unidentified friend that he was unable to sleep or eat because he had “fallen in love” with Barahona, the report states.

Once Miguel was born, Barahona strangely dressed him in pink and described him as a girl in Facebook photos — which enraged Infante, he told cops Tuesday.

He rambled about the devil, and told cops he did an “evil deed,” police sources said.

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He said he killed the two because he was angry over the way she was raising the boy, sources said.

Infante griped about child-support payments, sources said. He paid $80 to $100 weekly and had visitation rights with Miguel, who relatives said loved Thomas the Tank Engine.

Source said Infante lied to detectives that he wasn’t at the building where the bodies were found.

He was seen going in and out of the six-story residence, including one recent day when he changed clothes while inside, sources said.

Infante was supposed spend Christmas with Barahona, their son and Barahona’s mom at the mother’s house on West 56th Street, but he never showed, sources said.

Infante has no criminal record or history of mental illness. He worked at an airport near the Pennsylvania-New Jersey border, said sources, who had no further details.

Barahona, an Afghanistan war vet who was making $73,000 a year when she was fired in 2013, calls herself “divorced” on her Facebook page — which features her favorite quote: “Never give up!”

The mother of two — whose 8-year-old daughter by another man lives with her grandmother in Hell’s Kitchen — was pursuing a degree in forensic science at John Jay College of Criminal Justice.

Neighbors of Barahona’s mother, a retired teacher, said workers for the city’s Administration for Children’s Services picked up the young girl Tuesday morning.

“We are deeply committed to ensuring the safety and well-being of our city’s children. ACS, along with NYPD, is currently investigating this matter,” said ACS spokesperson Jose Bayona, who declined to comment when asked about the daughter being taken into custody.

The spokesman also would not say if there was a case file open in regards to Miguel.

Barahona’s brother, Jaime Bravo, 29, said he “was shocked more than anything else” when he learned the gruesome news.

“She was shy but closed, but you can’t really blame her,” Bravo said. “She had just gone through some pretty risky things,” he said, referring to his sister’s sex scandal and firing.

He said the family is trying to “shield” his sister’s daughter from the murders.